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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Restarting after BAM pairing #517

Closed pna059 closed 2 years ago

pna059 commented 2 years ago

Hi, my HiC-pro run (with singularity) has stopped right after BAM file pairing. The last LOG file is the mergeSAM.log bowtie results sem to be in place including the .bwt2pairs.bam and .bwt2pairs.pairstat being the last output files When I attempt to continue from the stage -s quality_checks it runs only the R output and the stats plot. When running from -s proc_hic, the error says: Exit: Error: Directory Hierarchy of rawdata '/storage/budejovice1/home/pavlan/Morex_HiChIP/24DAP/H3K4me3_1' is not correct. Paired '.bam' files with _R1/_R2 are required for 'proc_hic' step(s)

Do I need to reorganize the files in order to start from the second step? I really don`t want to run the mapping again, my genome and data files are big.

Thanks for the help!

pna059 commented 2 years ago

I solved the issue by changing the -i to the previous step results directory, specifically the 'bowtie_results/bwt2' for proc_hic and quality_checks. For steps merge_persamples and build_contact_maps, the -i is 'hic_results/data/' and for ise_norm step it is 'hic_results/matrix.